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HDBR Abnormal Fetal Samples Exome Sequencing Data

The HDBR (www.hdbr.org) is a human embryonic and fetal tissue bank supplying registered researchers with access to these valuable research materials up to 22 weeks post-conception (PCW [PMC4640175]). All of the samples collected are analysed for chromosomal abnormalities, and all samples with an abnormal phenotype are either analysed by SNP array, or exome sequenced. These datasets are generated from those abnormal samples that have been analysed by exome sequencing. To request access to this data, or if any researcher is interested in obtaining tissue from any of the samples HDBR collect, please email enquiries@hdbr.org.

Study ID EGAS00001006300

Dataset 1 - May 2022 EGAD00001008825

Exome sequencing data from seven phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2.

Samples used:

Description HDBR ID Phenotype EGA ID Alias Gender Tissue used
Human fetus, 18 PCW   15832

Abnormal left hand & no right foot

 EGAN00003552578 11_15832_18PCW male skin
Human fetus, 12 PCW   15854 Face and heart abnormal EGAN00003552570 3_15854_12PCW male skin
Human fetus, 21 PCW
(sample a)  		 15861 Cleft palate/lip EGAN00003552579 8_15861_21PCW_A male skin
Human fetus, 21 PCW
(sample b)  		 15861 Cleft palate/lip EGAN00003552571 12_15861_21PCW_B male skin
Human fetus, 17 PCW
(sample a)  		 15862 Coarctation of aorta EGAN00003552577 2_15862_17PCW_A male skin
Human fetus, 17 PCW
(sample b)  		 15862 Coarctation of aorta EGAN00003552580 9_15862_17PCW_B male skin
Human fetus, 12 PCW
(sample a)		 15887 Retinitis pigmentosa EGAN00003552574 5_15887_12PCW_A female unknown
Human fetus, 12 PCW
(sample b)		 15887 Retinitis pigmentosa EGAN00003552572 6_15887_12PCW_B female unknown
Human fetus, 17 PCW 15922 No tibia or fibula EGAN00003552573 7_15922_17PCW male skin
Human fetus, 15 PCW
(sample a)		 15930 Exomphalos major EGAN00003552575 1_15930_15PCW_A male skin
Human fetus, 15 PCW
(sample b)		 15930 Exomphalos major EGAN00003552576 10_15930_15PCW_B male skin

 

Dataset 2 - November 2022 EGAD00001009715

Exome sequencing data from thirteen phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2.

Samples used:

Description HDBR ID Phenotype EGA ID Alias Gender Tissue used
Human fetus, 16 PCW   16382

Potential Menkes Syndrome

 EGAN00004189521 44_16382_16PCW male skin
Human fetus, 16 PCW   16355 Cleft Palate and Aortic Bridge EGAN00004189522 43_16355_16PCW male skin
Human fetus, 14 PCW   16266 Down's Syndrome EGAN00004189523 42_16266_14PCW male skin
Human embryo, CS23 16050 Neural tube Defect and Cleft Palate EGAN00004189524 41_16050_CS23 male chorionic villi
Human fetus, 19 PCW 16191 Talipes equinovarus EGAN00004189525 40_16191_19PCW male skin
Human fetus, 20 PCW 16312 Spina Bifida EGAN00004189526 39_16312_20PCW female skin
Human embryo, CS19 16362 Cleft Lip and Microcephaly EGAN00004189527 38_16362_CS19 male skin
Human fetus, 21 PCW 16128 Cardiac Defects EGAN00004189528 37_16128_21PCW male skin
Human fetus, 11 PCW 15973 Gastroschisis EGAN00004189529 36_15973_11PCW male skin
Human fetus, 16 PCW 15992 Spina Bifida EGAN00004189530 35_15992_16PCW male skin
Human fetus, 11 PCW 16067 Beta Thalassemia Major by Congenital Varicella Syndrome EGAN00004189531 34_16067_11PCW female skin
Human fetus, 15 PCW 16012 Syndactyly and Talipes equinovarus EGAN00004189532 33_16012_15PCW female skin
Human embryo, CS19 16061 Anencephaly Midbrain EGAN00004189533 32_16061_CS19 female limb

 

Dataset 3 - August 2024 EGAD50000000722

Exome sequencing data from fourteen phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2.

Samples used:

Description HDBR ID Phenotype EGA ID Alias Gender Tissue used
Human fetus, 12 PCW 17745 Anencephaly EGAN50000095689 8_17745 female skin
Human fetus, 19 PCW   16425 Bilateral megaventricular condition EGAN50000095690 3_16425 male skin
Human fetus, 12 PCW 16558 Acrania EGAN50000095691 13_16588 female skin
Human fetus, 20 PCW 16507 Sickle cell EGAN50000095692 5_16507 male skin
Human fetus, 17 PCW   16453 Sickle cell EGAN50000095693 4_16453 male skin
Human embryo, CS16 17905 Potential Spina Bifida EGAN50000095694 12_17905 female liver
Human fetus, 15 PCW 16368 Cystic hygroma EGAN50000095695 11_16368 female skin
Human fetus, 21 PCW   16500

Hypoplastic left heart syndrome

 EGAN50000095696 1_16500 female skin
Human fetus, 13 PCW 16529 Acrania and Unilateral cleft palate EGAN50000095697 10_16529 female muscle
Human fetus, 11 PCW 17601 Ponton cerebellar hypoplasia Type 1B EGAN50000095698 6_17601 female skin
Human fetus, 13 PCW 17893 Norrie disease EGAN50000095699 9_17893 male skin
Human fetus, 15 PCW   16468 Severe Oligohydramnios EGAN50000095700 2_16468 female skin
Human fetus, 12 PCW 17896 Acrania EGAN50000095701 7_17896 female skin
Human fetus, 14 PCW 17827 Alport syndrome EGAN50000095702 14_17827 male muscle

 

Dataset 4 - December 2024 EGAD50000001809

Exome sequencing data from sixteen phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2.

Samples used:

Description HDBR ID Phenotype EGA ID Alias Gender Tissue used
Human fetus, 11 PCW 18319 Caudal regression, abnormal limb EGAN50000278865 17_18319_11pcw female skin
Human fetus, 12 PCW   18247 Huntington's disease EGAN50000278866 13_18247_12pcw male skin
Human fetus, 18 PCW 18270 Cleft palate EGAN50000278867 16_18270_18pcw male skin
Human fetus, 13 PCW 18146 Tetralogy of fallot EGAN50000278868 11_18146_13pcw female skin
Human embryo, CS17  17973 Spina Bifida EGAN50000278869 8_17973_CS17 female lung
Human fetus, 11 PCW 18251 Heart defects EGAN50000278870 14_18251_11pcw female skin
Human fetus, stage unknown 17924 Growth distortion EGAN50000278871 6_17924_NA male skin
Human fetus, 9 PCW   18398

Bowel protrudes from abdomen and thick neck

 EGAN50000278872 19_18398_9pcw female skin
Human fetus, 13 PCW 18148 Cystic hygroma, megacystic bladder, bilaterally enlarged kidneys EGAN50000278873 20_18148 male skin
Human fetus, 12 PCW 17969 Heart abnormalities EGAN50000278874 7_17969_12pcw male adrenal
Human embryo, CS21 18349 Large liver, eyes wide and palate not fused. Small lower limbs, toes still webbed EGAN50000278875 18_18349_CS21 male placenta
Human fetus, 12 PCW   18019 Exomphalos major (bowel stomach liver) EGAN50000278876 9_18019_12pcw female brain
Human fetus, 17 PCW 18258 Sickle Cell EGAN50000278877 15_18258_17pcw female skin
Human fetus, Late 8PCW 18094 Anencephaly EGAN50000278878 21_18094 female skin
Human fetus, 17 PCW 18193 An unusual peak pattern seen in one of the chromosome 16 microsatellite markers D16S753 (16p11.2) EGAN50000278879 12_18193_17pcw female skin
Human fetus, 13 PCW 18053 Suspected T21 but typical karyotype EGAN50000278880 10_18053_13pcw female skin